rs10088180
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000523491.1(NATP):n.1A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.649 in 153,810 control chromosomes in the GnomAD database, including 33,032 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.65 ( 33002 hom., cov: 32)
Exomes 𝑓: 0.15 ( 30 hom. )
Consequence
NATP
ENST00000523491.1 non_coding_transcript_exon
ENST00000523491.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.53
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NATP | ENST00000523491.1 | n.1A>G | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.654 AC: 99457AN: 151962Hom.: 32992 Cov.: 32
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GnomAD4 exome AF: 0.147 AC: 254AN: 1730Hom.: 30 Cov.: 0 AF XY: 0.178 AC XY: 174AN XY: 980
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GnomAD4 genome ? AF: 0.654 AC: 99508AN: 152080Hom.: 33002 Cov.: 32 AF XY: 0.646 AC XY: 48006AN XY: 74344
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at